5VIV | pdb_00005viv

Crystal structure of monomeric near-infrared fluorescent protein miRFP670

• PDB DOI: https://doi.org/10.2210/pdb5VIV/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Rhodopseudomonas palustris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-17 Released: 2017-06-21 
• Deposition Author(s): Pletnev, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 
  0.189 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.150 (Depositor) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies.

Baloban, M., Shcherbakova, D.M., Pletnev, S., Pletnev, V.Z., Lagarias, J.C., Verkhusha, V.V.

(2017) Chem Sci 8: 4546-4557

• PubMed: 28936332 
• DOI: https://doi.org/10.1039/c7sc00855d
• Primary Citation Related Structures: 
  5VIK, 5VIQ, 5VIV


• PubMed Abstract: 
  

  Brighter near-infrared (NIR) fluorescent proteins (FPs) are required for multicolor microscopy and deep-tissue imaging. Here, we present structural and biochemical analyses of three monomeric, spectrally distinct phytochrome-based NIR FPs, termed miRFPs. The miRFPs are closely related and differ by only a few amino acids, which define their molecular brightness, brightness in mammalian cells, and spectral properties. We have identified the residues responsible for the spectral red-shift, revealed a new chromophore bound simultaneously to two cysteine residues in the PAS and GAF domains in blue-shifted NIR FPs, and uncovered the importance of amino acid residues in the N-terminus of NIR FPs for their molecular and cellular brightness. The novel chromophore covalently links the N-terminus of NIR FPs with their C-terminal GAF domain, forming a topologically closed knot in the structure, and also contributes to the increased brightness. Based on our studies, we suggest a strategy to develop spectrally distinct NIR FPs with enhanced brightness.

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Organizational Affiliation: 
• Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center , Albert Einstein College of Medicine , Bronx , New York 10461 , USA . Email: [e-mail].
Macromolecular Crystallography Laboratory , National Cancer Institute , Leidos Biomedical Research Inc. , Basic Research Program , Argonne , Illinois 60439 , USA.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences , Moscow 117997 , Russian Federation.
Department of Molecular and Cellular Biology , University of California in Davis , California 95616 , USA.
Department of Biochemistry and Developmental Biology , Faculty of Medicine , University of Helsinki , Helsinki 00029 , Finland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.78 kDa 
• Atom Count: 2,878 
• Modeled Residue Count: 301 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
monomeric near-infrared fluorescent protein miRFP670	A	315	Rhodopseudomonas palustris	Mutation(s): 0
UniProt
Find proteins for A0A161I5N6 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore A0A161I5N6  Go to UniProtKB:  A0A161I5N6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9V1	C [auth A]	3-[2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl] methyl]-5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]pro panoic acid C33 H40 N4 O6 FCSIENOPZMSJPT-WOJBJXKFSA-N
9UY	B [auth A]	3-[5-[[(3~{R},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid C33 H38 N4 O6 IAVYOZQSRLDKLE-WOJBJXKFSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.189 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.150 (Depositor) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.539	α = 90
b = 53.282	β = 90
c = 107.397	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Pletnev, S.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2024-10-16
  Changes: Structure summary